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Gromacs User Manual GROMACS USER MANUAL Groningen Machine for Chemical Simulations Version 3.1 GROMACS USER MANUAL Version 3.1 David van der Spoel Aldert R. van Buuren Emile Apol Pieter J. Meulenhoff D. Peter Tieleman Alfons L.T.M. Sijbers Berk Hess K. Anton Feenstra Erik Lindahl Rudi van Drunen Herman J.C. Berendsen c 1991–2002 Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. iv Preface & Disclaimer This manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is meant as a source of information and references for the GROMACS user. It covers both the physical background of MD simulations in general and details of the GROMACS software in particular. The manual is continuously being worked on, which in some cases might mean the information is not entirely correct. When citing this document in any scientific publication please refer to it as: D. van der Spoel, A. R. van Buuren, E. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, B. Hess, K. A. Feenstra, E. Lindahl, R. van Drunen and H. J. C. Berendsen, Gromacs User Manual version 3.1, Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet: www.gromacs.org (2002) or, if you use BibTeX, you can directly copy the following: @Manual{gmx31, title = "Gromacs {U}ser {M}anual version 3.1", author = "David van der Spoel and Aldert R. van Buuren and Emile Apol and Pieter J. Meulen\-hoff and D. Peter Tieleman and Alfons L. T. M. Sij\-bers and Berk Hess and K. Anton Feenstra and Erik Lindahl and Rudi van Drunen and Herman J. C. Berendsen", address= "Nij\-enborgh 4, 9747 AG Groningen, The Netherlands. Internet: http://www.gromacs.org", year = "2001" } We humbly ask that you cite the GROMACS papers [1, 2] when you publish your results. Any future development depends on academic research grants, since the package is distributed as free software! Comments are welcome, please send them by e-mail to [email protected]. Groningen, February 28, 2002. Department of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Fax: +31-503634800 v Online Resources You can find more documentation and other material at our homepage www.gromacs.org. Among other things there is an online reference, several GROMACS mailing lists with archives and con- tributed topologies/force fields. Manual and GROMACS versions We try to release an updated version of the manual whenever we release a new version of the soft- ware, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation. Any revision numbers (like 3.1.1) are however independent, to make it possible to implement bugfixes and manual improvements if necessary. GROMACS is Free Software The entire GROMACS package is available under the GNU General Public License. This means it’s free as in free speech, not just that you can use it without paying us money. For details, check the COPYING file in the source code or consult www.gnu.org/copyleft/gpl.html. The GROMACS source code and Linux packages are available on our homepage! vi Contents 1 Introduction 1 1.1 Computational Chemistry and Molecular Modeling ................ 1 1.2 Molecular Dynamics Simulations .......................... 2 1.3 Energy Minimization and Search Methods ..................... 5 2 Definitions and Units 7 2.1 Notation ....................................... 7 2.2 MD units ...................................... 7 2.3 Reduced units .................................... 9 3 Algorithms 11 3.1 Introduction ..................................... 11 3.2 Periodic boundary conditions ............................ 11 3.2.1 Some useful box types ........................... 13 3.2.2 Cutoff restrictions ............................. 14 3.3 The group concept ................................. 14 3.4 Molecular Dynamics ................................ 15 3.4.1 Initial conditions .............................. 15 3.4.2 Neighbor searching ............................. 18 3.4.3 Compute forces ............................... 20 3.4.4 Update configuration ............................ 21 3.4.5 Temperature coupling ........................... 22 3.4.6 Pressure coupling .............................. 24 3.4.7 Output step ................................. 28 3.5 Shell molecular dynamics .............................. 28 3.5.1 Optimization of the shell positions ..................... 28 viii Contents 3.6 Constraint algorithms ................................ 29 3.6.1 SHAKE ................................... 29 3.6.2 LINCS ................................... 30 3.7 Simulated Annealing ................................ 32 3.8 Stochastic Dynamics ................................ 32 3.9 Brownian Dynamics ................................ 33 3.10 Energy Minimization ................................ 33 3.10.1 Steepest Descent .............................. 33 3.10.2 Conjugate Gradient ............................. 34 3.11 Normal Mode Analysis ............................... 34 3.12 Free energy calculations .............................. 35 3.13 Essential Dynamics Sampling ........................... 37 3.14 Parallelization .................................... 37 3.14.1 Methods of parallelization ......................... 38 3.14.2 MD on a ring of processors ......................... 39 3.15 Parallel Molecular Dynamics ............................ 41 3.15.1 Domain decomposition ........................... 43 3.15.2 Domain decomposition for non-bonded forces ............... 43 3.15.3 Parallel PPPM ............................... 45 3.15.4 Parallel sorting ............................... 46 4 Force fields 49 4.1 Non-bonded interactions .............................. 50 4.1.1 The Lennard-Jones interaction ....................... 50 4.1.2 Buckingham potential ........................... 51 4.1.3 Coulomb interaction ............................ 52 4.1.4 Coulomb interaction with reaction field .................. 52 4.1.5 Modified non-bonded interactions ..................... 53 4.1.6 Modified short-range interactions with Ewald summation ......... 55 4.2 Bonded interactions ................................. 56 4.2.1 Bond stretching ............................... 56 4.2.2 Morse potential bond stretching ...................... 57 4.2.3 Cubic bond stretching potential ...................... 58 4.2.4 Harmonic angle potential .......................... 58 Contents ix 4.2.5 Cosine based angle potential ........................ 59 4.2.6 Improper dihedrals ............................. 59 4.2.7 Proper dihedrals .............................. 59 4.2.8 Special interactions ............................. 62 4.2.9 Position restraints .............................. 63 4.2.10 Angle restraints ............................... 64 4.2.11 Distance restraints ............................. 64 4.3 Free energy interactions ............................... 68 4.3.1 Soft-core interactions ............................ 70 4.4 Methods ....................................... 71 4.4.1 Exclusions and 1-4 Interactions. ...................... 71 4.4.2 Charge Groups. ............................... 72 4.4.3 Treatment of cutoffs ............................ 72 4.5 Dummy atoms. ................................... 73 4.6 Long Range Electrostatics ............................. 76 4.6.1 Ewald summation .............................. 76 4.6.2 PME .................................... 77 4.6.3 PPPM .................................... 77 4.6.4 Optimizing Fourier transforms ....................... 78 4.7 All-hydrogen forcefield ............................... 79 4.8 GROMOS-96 notes ................................. 79 4.8.1 The GROMOS-96 force field ........................ 79 4.8.2 GROMOS-96 files ............................. 80 5 Topologies 81 5.1 Introduction ..................................... 81 5.2 Particle type ..................................... 81 5.2.1 Atom types ................................. 82 5.2.2 Dummy atoms ............................... 83 5.3 Parameter files ................................... 84 5.3.1 Atoms .................................... 84 5.3.2 Bonded parameters ............................. 85 5.3.3 Non-bonded parameters .......................... 86 5.3.4 1-4 interactions ............................... 87 x Contents 5.3.5 Exclusions ................................. 87 5.4 Constraints ..................................... 87 5.5 Databases ...................................... 88 5.5.1 Residue database .............................. 88 5.5.2 Hydrogen database ............................. 90 5.5.3 Termini database .............................. 91 5.6 File formats ..................................... 93 5.6.1 Topology file ................................ 93 5.6.2 Molecule.itp file .............................. 98 5.6.3 Ifdef option ................................. 100 5.6.4 Free energy calculations .......................... 101 5.6.5 Constraint force ............................... 102 5.6.6 Coordinate file ............................... 103 6 Special Topics 105 6.1 Calculating potentials of mean force: the pull code ................ 105 6.1.1 Overview .................................. 105 6.1.2 Usage .................................... 106 6.1.3 Output ................................... 109 6.1.4 Limitations ................................. 109 6.1.5 Implementation ............................... 110 6.1.6 Future development ............................. 110 6.2 Removing fastest degrees of freedom
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